[Mne_analysis] maxfilter for head movement compensation only

Eric Larson larson.eric.d at gmail.com
Mon May 6 13:33:17 EDT 2019
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>    1. Head position extraction using Electa's MaxFilter
>       1. Is this step sensitive to noisy/flat channels if I only need
>       head position?
>       2. Is it necessary/advised to use -cal and -ctc files for this
>       purpose?
> During recordings, the HPI coils emit sinusoids, and these are picked up
by the MEG channels. From this recording, the amplitudes on each channel
are estimated. From these amplitudes, coil locations are estimated. So if
there is some channel that is bad, it could (probably only slightly) bias
the position estimation step. So better to exclude bad channels even before
head position estimation if possible.

Regarding fine calibration and cross-talk, I'm not sure if MaxFilter makes
use of them in the computed magnetic dipole forward model or not. My guess
is that it does not. (I suppose you could check to see if the positions are
numerically identical with and without fine calibration and cross-talk to
check, if you want.) Even if it does use them, the difference will probably
be minimal.

>    1. Head movement compensation using mne-python's maxwell_filter
>    1. Is this step sensitive to noisy/flat channels if I only do movement
>       compensation?
>       2. Is it necessary/advised to use the fine calibration and
>       cross-talk cancellation files for this?
>       3. What parameters should I supply to maxwell_filter to limit it to
>       head movement compensation?
> Currently there is no way to do just movement compensation without also
maxwell filtering (reducing rank / denoising). In principle it should be
possible to do this without rank reduction (see this GitHub issue
<https://github.com/mne-tools/mne-python/issues/6085> if you want to track
our progress here) but it is not implemented yet, and there will probably
be a reduction in the resulting signal-to-noise ratio due to reconstruction

I remove bad channels/epochs at a later stage using the autoreject package.

One reproducible option would be to use autoreject or some other automated
routine to determine bad channels. MaxFilter even has an `autobad` option
you could try running before the head position estimation step to get a
list of bad channels. In principle you should be able to combine head
position estimation -headpos and automatic bad channel detection -autobad,
but in practice you can encounter bugs this way, so it's safer to separate
it into two steps.

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